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annotate hivclustering.xml @ 2:9dc36a1975e8 draft

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planemo upload for repository https://github.com/veg/hivclustering/ commit b'a6d09759f16c40d4607d30f4bb28772e74c07021\n'-dirty
author rdvelazquez
date Thu, 19 Apr 2018 14:39:39 -0400
parents d975f8166fc8
children 8a6f3d2a2d23
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1 <?xml version="1.0"?>
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2 <tool id="hivclustering" name="Make inferences" version="@VERSION@.0">
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3 <description>on HIV-1 transmission networks using HIVClustering</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 hivnetworkcsv --input $input $cluster $multiple_edges $singletons $centralities
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10 --threshold $threshold --exclude $exclude --triangles $triangles --format $format
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11 #if $contamination.contaminants != 'ignore':
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12 --contaminants $contamination.contaminants
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13 --contaminant-file '$contamination.contaminant_file'
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14 #end if
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15 #if $edges.edge_filtering != 'ignore':
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16 --edge-filtering $edges.edge_filtering
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17 --sequences $sequences
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18 #end if
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19 #if $uds:
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20 --uds $uds
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21 #end if
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22 #if $edi:
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23 --edi $edi
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24 #end if
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25 #if $old_edi:
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26 --old_edi $old_edi
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27 #end if
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28 #if $resistance:
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29 --resistance $resistance
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30 #end if
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31 #if $attributes:
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32 --attributes $attributes
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33 #end if
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34 #if $filter:
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35 --filter '$filter'
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36 #end if
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37 --json > hivcluster.json
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38 ]]>
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39 </command>
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40 <inputs>
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41 <param argument="--input" type="data" format="csv" multiple="True" label="Input file with inferred links"/>
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42 <conditional name="contamination">
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43 <param argument="--contaminants" type="select" label="How to treat contamination">
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44 <option value="ignore" selected="True">Do nothing</option>
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45 <option value="report">Report</option>
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46 <option value="remove">Remove</option>
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47 </param>
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48 <when value="ignore"/>
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49 <when value="report">
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50 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
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51 </when>
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52 <when value="remove">
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53 <param name="contaminant_file" argument="--contaminant-file" type="data" format="tabular" label="Input file with contaminant IDs"/>
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54 </when>
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55 </conditional>
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56 <conditional name="edges">
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57 <param name="edge_filtering" argument="--edge-filtering" type="select" label="Compute edge support and mark edges">
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58 <option value="ignore" selected="True">Do not mark</option>
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59 <option value="report">For display</option>
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60 <option value="remove">For removal</option>
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61 </param>
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62 <when value="ignore"/>
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63 <when value="report">
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64 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/>
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65 </when>
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66 <when value="remove">
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67 <param argument="--sequences" type="data" format="fasta" multiple="True" label="Input multi-sequence alignment"/>
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68 </when>
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69 </conditional>
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70 <param argument="--uds" type="data" format="csv" optional="True" label="Input file with UDS data"/>
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71 <param argument="--edi" type="data" format="json" optional="True" label="Input JSON with clinical information"/>
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72 <param argument="--old_edi" type="data" format="csv" optional="True" label="Legacy EDI dates in CSV format"/>
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73 <param argument="--resistance" type="data" format="csv" optional="True" label="Resistance annotation in JSON format"/>
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74 <param argument="--attributes" type="data" format="csv" optional="True" label="Input CSV with node attributes"/>
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75 <param argument="--filter" type="data" format="text" optional="True" label="File with IDs to cluster, one per line"/>
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76 <param argument="--format" type="select" label="Sequence ID format">
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77 <option value="AEH">AEH</option>
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78 <option value="LANL">LANL</option>
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79 <option value="plain">plain</option>
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80 </param>
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81 <param argument="--cluster" type="boolean" truevalue="--cluster hivcluster.csv" falsevalue="" label="Output a CSV file with cluster assignments for each sequence"/>
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82 <param name="multiple_edges" argument="--multiple-edges" type="boolean" truevalue="--multiple-edges" falsevalue="" label="Permit multiple edges to link the same pair of nodes in the network"/>
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83 <param argument="--singletons" type="boolean" truevalue="--singletons" falsevalue="" label="Include singletons in output"/>
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84 <param argument="--centralities" type="boolean" truevalue="--centralities" falsevalue="" label="Output a CSV file with node centralities"/>
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85 <param argument="--threshold" type="float" value="0.015" label="Only count edges where the distance is less than this threshold"/>
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86 <param argument="--exclude" type="integer" value="1959" label="Only consider sequences isolated after this year"/>
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87 <param argument="--triangles" type="integer" value="65536" label="Maximum number of triangles to consider in each filtering pass"/>
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88 </inputs>
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89 <outputs>
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90 <data name="graph" from_work_dir="hivcluster.json" format="hivtrace"/>
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91 </outputs>
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92 <tests>
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93 <test>
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94 <param name="input" value="hivclustering-in1.csv" ftype="csv"/>
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95 <param name="format" value="plain"/>
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96 <param name="threshold" value="0.8"/>
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97 <param name="json" value="True"/>
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98 <output name="graph" ftype="hivtrace">
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99 <assert_contents>
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100 <has_text text="Cluster sizes"/>
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101 </assert_contents>
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102 </output>
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103 </test>
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104 <test>
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105 <param name="input" value="hivclustering-in2.csv" ftype="csv"/>
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106 <param name="format" value="plain"/>
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107 <param name="threshold" value="0.8"/>
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108 <param name="json" value="True"/>
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109 <output name="graph" ftype="hivtrace">
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110 <assert_contents>
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111 <has_text text="Cluster sizes"/>
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112 </assert_contents>
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113 </output>
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114 </test>
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115 </tests>
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116 <help><![CDATA[
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117 HIVClustering
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118 -------------
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119
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120 A python library that makes inferences on HIV-1 transmission networks.
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121 ]]></help>
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122 <expand macro="citations"/>
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123 </tool>